}
}
-/*! \brief Build the index that maps each local atom to its local atom group */
-static void makeLocalAtomGroupsFromAtoms(gmx_domdec_t *dd)
-{
- const gmx::RangePartitioning &atomGrouping = dd->atomGrouping();
-
- dd->localAtomGroupFromAtom.clear();
-
- for (size_t g = 0; g < dd->globalAtomGroupIndices.size(); g++)
- {
- for (int gmx_unused a : atomGrouping.block(g))
- {
- dd->localAtomGroupFromAtom.push_back(g);
- }
- }
-}
-
-/*! \brief Returns the squared distance between charge groups \p i and \p j */
-static real dd_dist2(t_pbc *pbc_null, rvec *cg_cm, const int *la2lc, int i, int j)
+/*! \brief Returns the squared distance between atoms \p i and \p j */
+static real dd_dist2(t_pbc *pbc_null, const rvec *x, const int i, int j)
{
rvec dx;
if (pbc_null)
{
- pbc_dx_aiuc(pbc_null, cg_cm[la2lc[i]], cg_cm[la2lc[j]], dx);
+ pbc_dx_aiuc(pbc_null, x[i], x[j], dx);
}
else
{
- rvec_sub(cg_cm[la2lc[i]], cg_cm[la2lc[j]], dx);
+ rvec_sub(x[i], x[j], dx);
}
return norm2(dx);
const gmx_molblock_t *molb,
gmx_bool bRCheckMB, const ivec rcheck, gmx_bool bRCheck2B,
real rc2,
- int *la2lc,
t_pbc *pbc_null,
rvec *cg_cm,
const t_iparams *ip_in,
tiatoms[2] = entry->la;
/* If necessary check the cgcm distance */
if (bRCheck2B &&
- dd_dist2(pbc_null, cg_cm, la2lc,
+ dd_dist2(pbc_null, cg_cm,
tiatoms[1], tiatoms[2]) >= rc2)
{
bUse = FALSE;
*/
if (rcheck[d] &&
k_plus[d] &&
- dd_dist2(pbc_null, cg_cm, la2lc,
+ dd_dist2(pbc_null, cg_cm,
tiatoms[k_zero[d]], tiatoms[k_plus[d]]) >= rc2)
{
bUse = FALSE;
const std::vector<gmx_molblock_t> &molb,
gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
real rc2,
- int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
+ t_pbc *pbc_null, rvec *cg_cm,
const t_iparams *ip_in,
t_idef *idef,
int izone,
dd, zones,
&molb[mb],
bRCheckMB, rcheck, bRCheck2B, rc2,
- la2lc,
pbc_null,
cg_cm,
ip_in,
dd, zones,
&molb[mb],
bRCheckMB, rcheck, bRCheck2B, rc2,
- la2lc,
pbc_null,
cg_cm,
ip_in,
}
/*! \brief Set the exclusion data for i-zone \p iz for the case of no exclusions */
-static void set_no_exclusions_zone(const gmx_domdec_t *dd,
- const gmx_domdec_zones_t *zones,
+static void set_no_exclusions_zone(const gmx_domdec_zones_t *zones,
int iz,
t_blocka *lexcls)
{
- const auto zone = dd->atomGrouping().subRange(zones->cg_range[iz],
- zones->cg_range[iz + 1]);
-
- for (int a : zone)
+ for (int a = zones->cg_range[iz]; a < zones->cg_range[iz + 1]; a++)
{
lexcls->index[a + 1] = lexcls->nra;
}
static int make_exclusions_zone_cg(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
const std::vector<gmx_moltype_t> &moltype,
gmx_bool bRCheck, real rc2,
- int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
+ t_pbc *pbc_null, rvec *cg_cm,
const int *cginfo,
t_blocka *lexcls,
int iz,
const gmx_ga2la_t &ga2la = *dd->ga2la;
- const auto jRange =
- dd->atomGrouping().subRange(zones->izone[iz].jcg0,
- zones->izone[iz].jcg1);
+ // TODO: Replace this by a more standard range
+ const gmx::RangePartitioning::Block jRange(zones->izone[iz].jcg0,
+ zones->izone[iz].jcg1);
n_excl_at_max = dd->reverse_top->n_excl_at_max;
/* We set the end index, but note that we might not start at zero here */
- lexcls->nr = dd->atomGrouping().subRange(0, cg_end).size();
+ lexcls->nr = cg_end;
int n = lexcls->nra;
int count = 0;
- for (int cg = cg_start; cg < cg_end; cg++)
+ for (int la = cg_start; la < cg_end; la++)
{
if (n + (cg_end - cg_start)*n_excl_at_max > lexcls->nalloc_a)
{
lexcls->nalloc_a = over_alloc_large(n + (cg_end - cg_start)*n_excl_at_max);
srenew(lexcls->a, lexcls->nalloc_a);
}
- const auto atomGroup = dd->atomGrouping().block(cg);
- if (GET_CGINFO_EXCL_INTER(cginfo[cg]) ||
- !GET_CGINFO_EXCL_INTRA(cginfo[cg]))
+ if (GET_CGINFO_EXCL_INTER(cginfo[la]) ||
+ !GET_CGINFO_EXCL_INTRA(cginfo[la]))
{
/* Copy the exclusions from the global top */
- for (int la : atomGroup)
+ lexcls->index[la] = n;
+ int a_gl = dd->globalAtomIndices[la];
+ int a_mol;
+ global_atomnr_to_moltype_ind(dd->reverse_top, a_gl, &mb, &mt, &mol, &a_mol);
+ excls = &moltype[mt].excls;
+ for (int j = excls->index[a_mol]; j < excls->index[a_mol+1]; j++)
{
- lexcls->index[la] = n;
- int a_gl = dd->globalAtomIndices[la];
- int a_mol;
- global_atomnr_to_moltype_ind(dd->reverse_top, a_gl, &mb, &mt, &mol, &a_mol);
- excls = &moltype[mt].excls;
- for (int j = excls->index[a_mol]; j < excls->index[a_mol+1]; j++)
+ int aj_mol = excls->a[j];
+ /* Since exclusions are pair interactions,
+ * just like non-bonded interactions,
+ * they can be assigned properly up
+ * to the DD cutoff (not cutoff_min as
+ * for the other bonded interactions).
+ */
+ if (const auto *jEntry = ga2la.find(a_gl + aj_mol - a_mol))
{
- int aj_mol = excls->a[j];
- /* This computation of jla is only correct intra-cg */
- int jla = la + aj_mol - a_mol;
- if (atomGroup.inRange(jla))
+ if (iz == 0 && jEntry->cell == 0)
{
- /* This is an intra-cg exclusion. We can skip
- * the global indexing and distance checking.
- */
- /* Intra-cg exclusions are only required
- * for the home zone.
- */
- if (iz == 0)
+ lexcls->a[n++] = jEntry->la;
+ /* Check to avoid double counts */
+ if (jEntry->la > la)
{
- lexcls->a[n++] = jla;
- /* Check to avoid double counts */
- if (jla > la)
- {
- count++;
- }
+ count++;
}
}
- else
+ else if (jRange.inRange(jEntry->la) &&
+ (!bRCheck ||
+ dd_dist2(pbc_null, cg_cm, la, jEntry->la) < rc2))
{
- /* This is a inter-cg exclusion */
- /* Since exclusions are pair interactions,
- * just like non-bonded interactions,
- * they can be assigned properly up
- * to the DD cutoff (not cutoff_min as
- * for the other bonded interactions).
- */
- if (const auto *jEntry = ga2la.find(a_gl + aj_mol - a_mol))
- {
- if (iz == 0 && jEntry->cell == 0)
- {
- lexcls->a[n++] = jEntry->la;
- /* Check to avoid double counts */
- if (jEntry->la > la)
- {
- count++;
- }
- }
- else if (jRange.inRange(jEntry->la) &&
- (!bRCheck ||
- dd_dist2(pbc_null, cg_cm, la2lc, la, jEntry->la) < rc2))
- {
- /* jla > la, since jRange.begin() > la */
- lexcls->a[n++] = jEntry->la;
- count++;
- }
- }
+ /* jla > la, since jRange.begin() > la */
+ lexcls->a[n++] = jEntry->la;
+ count++;
}
}
}
}
else
{
- /* There are no inter-cg excls and this cg is self-excluded.
+ /* There are no inter-atomic excls and this atom is self-excluded.
* These exclusions are only required for zone 0,
* since other zones do not see themselves.
*/
if (iz == 0)
{
- for (int la : atomGroup)
- {
- lexcls->index[la] = n;
- for (int j : atomGroup)
- {
- lexcls->a[n++] = j;
- }
- }
- count += (atomGroup.size()*(atomGroup.size() - 1))/2;
+ lexcls->index[la] = n;
+ lexcls->a[n++] = la;
}
else
{
- /* We don't need exclusions for this cg */
- for (int la : atomGroup)
- {
- lexcls->index[la] = n;
- }
+ lexcls->index[la] = n;
}
}
}
const gmx_ga2la_t &ga2la = *dd->ga2la;
- const auto jRange =
- dd->atomGrouping().subRange(zones->izone[iz].jcg0,
- zones->izone[iz].jcg1);
+ // TODO: Replace this by a more standard range
+ const gmx::RangePartitioning::Block jRange(zones->izone[iz].jcg0,
+ zones->izone[iz].jcg1);
n_excl_at_max = dd->reverse_top->n_excl_at_max;
static void check_exclusions_alloc(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
t_blocka *lexcls)
{
- int nr = dd->atomGrouping().subRange(0, zones->izone[zones->nizone - 1].cg1).size();
+ const int nr = zones->izone[zones->nizone - 1].cg1;
check_alloc_index(lexcls, nr);
static void finish_local_exclusions(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
t_blocka *lexcls)
{
- const auto nonhomeIzonesAtomRange =
- dd->atomGrouping().subRange(zones->izone[0].cg1,
- zones->izone[zones->nizone - 1].cg1);
+ // TODO: Replace this by a more standard range
+ const gmx::RangePartitioning::Block nonhomeIzonesAtomRange(zones->izone[0].cg1,
+ zones->izone[zones->nizone - 1].cg1);
if (dd->n_intercg_excl == 0)
{
const int *cginfo,
gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
real rc,
- int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
+ t_pbc *pbc_null, rvec *cg_cm,
t_idef *idef,
t_blocka *lexcls, int *excl_count)
{
make_bondeds_zone(dd, zones,
mtop->molblock,
bRCheckMB, rcheck, bRCheck2B, rc2,
- la2lc, pbc_null, cg_cm, idef->iparams,
+ pbc_null, cg_cm, idef->iparams,
idef_t,
izone,
- dd->atomGrouping().subRange(cg0t, cg1t));
+ gmx::RangePartitioning::Block(cg0t, cg1t));
if (izone < nzone_excl)
{
excl_t->nra = 0;
}
- if (dd->atomGrouping().allBlocksHaveSizeOne() &&
- !rt->bExclRequired)
+ if (!rt->bExclRequired)
{
/* No charge groups and no distance check required */
make_exclusions_zone(dd, zones, mtop->moltype, cginfo,
rt->th_work[thread].excl_count =
make_exclusions_zone_cg(dd, zones,
mtop->moltype, bRCheck2B, rc2,
- la2lc, pbc_null, cg_cm, cginfo,
+ pbc_null, cg_cm, cginfo,
excl_t,
izone,
cg0t, cg1t);
*/
for (izone = nzone_excl; izone < zones->nizone; izone++)
{
- set_no_exclusions_zone(dd, zones, izone, lexcls);
+ set_no_exclusions_zone(zones, izone, lexcls);
}
finish_local_exclusions(dd, zones, lexcls);
return nbonded_local;
}
-void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs)
-{
- lcgs->nr = dd->globalAtomGroupIndices.size();
- lcgs->index = dd->atomGrouping_.rawIndex().data();
-}
-
void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
int npbcdim, matrix box,
rvec cellsize_min, const ivec npulse,
fprintf(debug, "Making local topology\n");
}
- dd_make_local_cgs(dd, <op->cgs);
-
bRCheckMB = FALSE;
bRCheck2B = FALSE;
}
if (bRCheckMB || bRCheck2B)
{
- makeLocalAtomGroupsFromAtoms(dd);
if (fr->bMolPBC)
{
pbc_null = set_pbc_dd(&pbc, fr->ePBC, dd->nc, TRUE, box);
}
dd->nbonded_local =
- make_local_bondeds_excls(dd, zones, &mtop, fr->cginfo,
+ make_local_bondeds_excls(dd, zones, &mtop, fr->cginfo.data(),
bRCheckMB, rcheck, bRCheck2B, rc,
- dd->localAtomGroupFromAtom.data(),
pbc_null, cgcm_or_x,
<op->idef,
<op->excls, &nexcl);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff